nci-cidc-schemas 0.26.37__py2.py3-none-any.whl → 0.27.0__py2.py3-none-any.whl

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Files changed (24) hide show
  1. cidc_schemas/__init__.py +1 -1
  2. cidc_schemas/json_validation.py +43 -0
  3. cidc_schemas/prism/merger.py +17 -8
  4. cidc_schemas/schemas/clinical_trial.json +3 -7
  5. cidc_schemas/schemas/participant.json +1 -3
  6. cidc_schemas/schemas/sample.json +178 -44
  7. cidc_schemas/schemas/shipping_core.json +74 -34
  8. cidc_schemas/schemas/templates/manifests/h_and_e_template.json +109 -13
  9. cidc_schemas/schemas/templates/manifests/microbiome_dna_template.json +111 -11
  10. cidc_schemas/schemas/templates/manifests/normal_blood_dna_template.json +102 -12
  11. cidc_schemas/schemas/templates/manifests/normal_tissue_dna_template.json +109 -13
  12. cidc_schemas/schemas/templates/manifests/pbmc_template.json +102 -93
  13. cidc_schemas/schemas/templates/manifests/plasma_template.json +101 -91
  14. cidc_schemas/schemas/templates/manifests/tissue_slide_template.json +109 -13
  15. cidc_schemas/schemas/templates/manifests/tumor_tissue_dna_template.json +109 -13
  16. cidc_schemas/schemas/templates/manifests/tumor_tissue_rna_template.json +109 -13
  17. cidc_schemas/template.py +1 -1
  18. cidc_schemas/unprism.py +4 -0
  19. {nci_cidc_schemas-0.26.37.dist-info → nci_cidc_schemas-0.27.0.dist-info}/METADATA +27 -16
  20. {nci_cidc_schemas-0.26.37.dist-info → nci_cidc_schemas-0.27.0.dist-info}/RECORD +24 -24
  21. {nci_cidc_schemas-0.26.37.dist-info → nci_cidc_schemas-0.27.0.dist-info}/WHEEL +1 -1
  22. {nci_cidc_schemas-0.26.37.dist-info → nci_cidc_schemas-0.27.0.dist-info}/LICENSE +0 -0
  23. {nci_cidc_schemas-0.26.37.dist-info → nci_cidc_schemas-0.27.0.dist-info}/entry_points.txt +0 -0
  24. {nci_cidc_schemas-0.26.37.dist-info → nci_cidc_schemas-0.27.0.dist-info}/top_level.txt +0 -0
cidc_schemas/schemas/templates/manifests/plasma_template.json CHANGED
@@ -41,16 +41,16 @@
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  "type_ref": "shipping_core.json#properties/tracking_number",
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  "allow_empty": true
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  },
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- "account number": {
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- "merge_pointer": "/account_number",
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- "type_ref": "shipping_core.json#properties/account_number",
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- "allow_empty": true
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- },
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  "shipping condition": {
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  "merge_pointer": "/shipping_condition",
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  "type_ref": "shipping_core.json#properties/shipping_condition",
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  "allow_empty": true
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  },
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+ "shipping condition other": {
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+ "merge_pointer": "/shipping_condition_other",
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+ "type_ref": "shipping_core.json#properties/shipping_condition_other",
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+ "allow_empty": true
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+ },
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  "date shipped": {
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  "merge_pointer": "/date_shipped",
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  "type_ref": "shipping_core.json#properties/date_shipped",
@@ -66,97 +66,90 @@
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  "type_ref": "shipping_core.json#properties/quality_of_shipment",
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  "allow_empty": true
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  },
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- "ship from": {
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- "merge_pointer": "/ship_from",
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- "type_ref": "shipping_core.json#properties/ship_from",
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+ "ship from sender person name": {
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+ "merge_pointer": "/ship_from_sender_person_name",
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+ "type_ref": "shipping_core.json#properties/ship_from_sender_person_name",
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  "allow_empty": true
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  },
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- "ship to": {
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- "merge_pointer": "/ship_to",
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- "type_ref": "shipping_core.json#properties/ship_to",
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+ "ship from sender email": {
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+ "merge_pointer": "/ship_from_sender_email",
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+ "type_ref": "shipping_core.json#properties/ship_from_sender_email",
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  "allow_empty": true
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- }
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- }
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- },
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-
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- "Essential Patient Data": {
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- "prism_preamble_object_schema": "clinical_trial.json",
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- "prism_preamble_object_pointer": "#",
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- "prism_data_object_pointer": "/participants/0/samples/0",
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- "data_columns": {
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- "Path Concordance Verification": {
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- "entry (#)": {
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- "do_not_merge": true,
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- "allow_empty": true,
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- "type": "string"
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- },
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- "participant ID": {
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- "merge_pointer": "2/participant_id",
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- "type_ref": "participant.json#properties/participant_id"
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- },
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- "CIMAC ID": {
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- "merge_pointer": "/cimac_id",
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- "type_ref": "sample.json#properties/cimac_id",
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- "process_as": [
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- {
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- "merge_pointer": "2/cimac_participant_id",
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- "type_ref": "participant.json#properties/cimac_participant_id",
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- "parse_through": "lambda x: x[:7]"
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- }
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- ]
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- },
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- "surgical pathology report id": {
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- "merge_pointer": "/surgical_pathology_report_id",
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- "type_ref": "sample.json#properties/surgical_pathology_report_id"
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- },
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- "clinical report id": {
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- "merge_pointer": "/clinical_report_id",
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- "type_ref": "sample.json#properties/clinical_report_id"
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- },
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- "collection event name": {
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- "merge_pointer": "/collection_event_name",
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- "type_ref": "sample.json#properties/collection_event_name"
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- },
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- "diagnosis verification": {
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- "merge_pointer": "/diagnosis_verification",
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- "type_ref": "sample.json#properties/diagnosis_verification"
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- }
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  },
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- "ICD-0-3 Code/Description": {
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- "Site Description": {
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- "merge_pointer": "/site_description",
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- "type_ref": "sample.json#properties/site_description"
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- },
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- "Topography Code": {
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- "merge_pointer": "/topography_code",
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- "type_ref": "sample.json#properties/topography_code"
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- },
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- "Topography Description": {
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- "merge_pointer": "/topography_description",
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- "type_ref": "sample.json#properties/topography_description"
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- },
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- "Histology/Behavior": {
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- "merge_pointer": "/histology_behavior",
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- "type_ref": "sample.json#properties/histology_behavior"
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- },
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- "Histology/Behavior Description": {
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- "merge_pointer": "/histology_behavior_description",
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- "type_ref": "sample.json#properties/histology_behavior_description"
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- }
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+ "ship from sender phone": {
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+ "merge_pointer": "/ship_from_sender_phone",
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+ "type_ref": "shipping_core.json#properties/ship_from_sender_phone",
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+ "allow_empty": true
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  },
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- "Demographics": {
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- "Sex": {
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- "merge_pointer": "2/gender",
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- "type_ref": "participant.json#properties/gender"
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- },
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- "Race": {
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- "merge_pointer": "2/race",
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- "type_ref": "participant.json#properties/race"
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- },
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- "Ethnic Group": {
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- "merge_pointer": "2/ethnicity",
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- "type_ref": "participant.json#properties/ethnicity"
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- }
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+ "ship from name": {
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+ "merge_pointer": "/ship_from_name",
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+ "type_ref": "shipping_core.json#properties/ship_from_name",
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+ "allow_empty": true
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+ },
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+ "ship from street1": {
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+ "merge_pointer": "/ship_from_street1",
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+ "type_ref": "shipping_core.json#properties/ship_from_street1",
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+ "allow_empty": true
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+ },
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+ "ship from street2": {
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+ "merge_pointer": "/ship_from_street2",
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+ "type_ref": "shipping_core.json#properties/ship_from_street2",
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+ "allow_empty": true
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+ },
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+ "ship from city": {
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+ "merge_pointer": "/ship_from_city",
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+ "type_ref": "shipping_core.json#properties/ship_from_city",
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+ "allow_empty": true
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+ },
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+ "ship from state": {
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+ "merge_pointer": "/ship_from_state",
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+ "type_ref": "shipping_core.json#properties/ship_from_state",
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+ "allow_empty": true
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+ },
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+ "ship from zip": {
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+ "merge_pointer": "/ship_from_zip",
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+ "type_ref": "shipping_core.json#properties/ship_from_zip",
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+ "allow_empty": true
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+ },
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+ "ship from country": {
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+ "merge_pointer": "/ship_from_country",
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+ "type_ref": "shipping_core.json#properties/ship_from_country",
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+ "allow_empty": true
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+ },
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+ "ship to name": {
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+ "merge_pointer": "/ship_to_name",
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+ "type_ref": "shipping_core.json#properties/ship_to_name",
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+ "allow_empty": true
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+ },
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+ "ship to street1": {
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+ "merge_pointer": "/ship_to_street1",
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+ "type_ref": "shipping_core.json#properties/ship_to_street1",
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+ "allow_empty": true
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+ },
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+ "ship to street2": {
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+ "merge_pointer": "/ship_to_street2",
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+ "type_ref": "shipping_core.json#properties/ship_to_street2",
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+ "allow_empty": true
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+ },
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+ "ship to city": {
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+ "merge_pointer": "/ship_to_city",
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+ "type_ref": "shipping_core.json#properties/ship_to_city",
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+ "allow_empty": true
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+ },
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+ "ship to state": {
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+ "merge_pointer": "/ship_to_state",
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+ "type_ref": "shipping_core.json#properties/ship_to_state",
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+ "allow_empty": true
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+ },
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+ "ship to zip": {
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+ "merge_pointer": "/ship_to_zip",
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+ "type_ref": "shipping_core.json#properties/ship_to_zip",
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+ "allow_empty": true
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+ },
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+ "ship to country": {
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+ "merge_pointer": "/ship_to_country",
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+ "type_ref": "shipping_core.json#properties/ship_to_country",
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+ "allow_empty": true
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  }
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  }
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  },
@@ -168,6 +161,8 @@
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  "data_columns": {
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  "IDs": {
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  "entry (#)": {
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+ "do_not_merge": true,
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+ "allow_empty": true,
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  "merge_pointer": "/shipping_entry_number",
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  "type_ref": "sample.json#properties/shipping_entry_number"
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  },
@@ -224,14 +219,29 @@
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  "merge_pointer": "/sample_collection_procedure",
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  "type_ref": "sample.json#properties/sample_collection_procedure"
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  },
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+ "sample collection procedure other": {
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+ "merge_pointer": "/sample_collection_procedure_other",
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+ "type_ref": "sample.json#properties/sample_collection_procedure_other",
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+ "allow_empty": true
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+ },
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  "type of primary container": {
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  "merge_pointer": "/type_of_primary_container",
229
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  "type_ref": "sample.json#properties/type_of_primary_container"
230
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  },
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+ "type of primary container other": {
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+ "merge_pointer": "/type_of_primary_container_other",
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+ "type_ref": "sample.json#properties/type_of_primary_container_other",
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+ "allow_empty": true
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+ },
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  "processed sample type": {
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  "merge_pointer": "/processed_sample_type",
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  "type_ref": "sample.json#properties/processed_sample_type"
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  },
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+ "processed sample quantity": {
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+ "merge_pointer": "/processed_sample_quantity",
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+ "type_ref": "sample.json#properties/processed_sample_quantity",
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+ "allow_empty": true
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+ },
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  "processed sample volume": {
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  "merge_pointer": "/processed_sample_volume",
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  "type_ref": "sample.json#properties/processed_sample_volume",
cidc_schemas/schemas/templates/manifests/tissue_slide_template.json CHANGED
@@ -41,16 +41,16 @@
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  "type_ref": "shipping_core.json#properties/tracking_number",
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  "allow_empty": true
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  },
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- "account number": {
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- "merge_pointer": "/account_number",
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- "type_ref": "shipping_core.json#properties/account_number",
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- "allow_empty": true
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- },
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  "shipping condition": {
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  "merge_pointer": "/shipping_condition",
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  "type_ref": "shipping_core.json#properties/shipping_condition",
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  "allow_empty": true
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  },
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+ "shipping condition other": {
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+ "merge_pointer": "/shipping_condition_other",
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+ "type_ref": "shipping_core.json#properties/shipping_condition_other",
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+ "allow_empty": true
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+ },
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  "date shipped": {
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  "merge_pointer": "/date_shipped",
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  "type_ref": "shipping_core.json#properties/date_shipped",
@@ -66,14 +66,89 @@
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  "type_ref": "shipping_core.json#properties/quality_of_shipment",
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  "allow_empty": true
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  },
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- "ship from": {
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- "merge_pointer": "/ship_from",
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- "type_ref": "shipping_core.json#properties/ship_from",
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+ "ship from sender person name": {
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+ "merge_pointer": "/ship_from_sender_person_name",
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+ "type_ref": "shipping_core.json#properties/ship_from_sender_person_name",
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+ "allow_empty": true
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+ },
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+ "ship from sender email": {
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+ "merge_pointer": "/ship_from_sender_email",
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+ "type_ref": "shipping_core.json#properties/ship_from_sender_email",
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  "allow_empty": true
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  },
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- "ship to": {
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- "merge_pointer": "/ship_to",
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- "type_ref": "shipping_core.json#properties/ship_to",
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+ "ship from sender phone": {
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+ "merge_pointer": "/ship_from_sender_phone",
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+ "type_ref": "shipping_core.json#properties/ship_from_sender_phone",
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+ "allow_empty": true
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+ },
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+ "ship from name": {
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+ "merge_pointer": "/ship_from_name",
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+ "type_ref": "shipping_core.json#properties/ship_from_name",
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+ "allow_empty": true
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+ },
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+ "ship from street1": {
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+ "merge_pointer": "/ship_from_street1",
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+ "type_ref": "shipping_core.json#properties/ship_from_street1",
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+ "allow_empty": true
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+ },
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+ "ship from street2": {
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+ "merge_pointer": "/ship_from_street2",
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+ "type_ref": "shipping_core.json#properties/ship_from_street2",
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+ "allow_empty": true
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+ },
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+ "ship from city": {
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+ "merge_pointer": "/ship_from_city",
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+ "type_ref": "shipping_core.json#properties/ship_from_city",
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+ "allow_empty": true
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+ },
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+ "ship from state": {
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+ "merge_pointer": "/ship_from_state",
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+ "type_ref": "shipping_core.json#properties/ship_from_state",
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+ "allow_empty": true
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+ },
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+ "ship from zip": {
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+ "merge_pointer": "/ship_from_zip",
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+ "type_ref": "shipping_core.json#properties/ship_from_zip",
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+ "allow_empty": true
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+ },
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+ "ship from country": {
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+ "merge_pointer": "/ship_from_country",
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+ "type_ref": "shipping_core.json#properties/ship_from_country",
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+ "allow_empty": true
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+ },
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+ "ship to name": {
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+ "merge_pointer": "/ship_to_name",
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+ "type_ref": "shipping_core.json#properties/ship_to_name",
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+ "allow_empty": true
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+ },
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+ "ship to street1": {
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+ "merge_pointer": "/ship_to_street1",
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+ "type_ref": "shipping_core.json#properties/ship_to_street1",
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+ "allow_empty": true
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+ },
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+ "ship to street2": {
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+ "merge_pointer": "/ship_to_street2",
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+ "type_ref": "shipping_core.json#properties/ship_to_street2",
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+ "allow_empty": true
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+ },
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+ "ship to city": {
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+ "merge_pointer": "/ship_to_city",
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+ "type_ref": "shipping_core.json#properties/ship_to_city",
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+ "allow_empty": true
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+ },
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+ "ship to state": {
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+ "merge_pointer": "/ship_to_state",
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+ "type_ref": "shipping_core.json#properties/ship_to_state",
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+ "allow_empty": true
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+ },
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+ "ship to zip": {
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+ "merge_pointer": "/ship_to_zip",
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+ "type_ref": "shipping_core.json#properties/ship_to_zip",
147
+ "allow_empty": true
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+ },
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+ "ship to country": {
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+ "merge_pointer": "/ship_to_country",
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+ "type_ref": "shipping_core.json#properties/ship_to_country",
77
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  "allow_empty": true
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  }
79
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  }
@@ -86,6 +161,8 @@
86
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  "data_columns": {
87
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  "IDs": {
88
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  "entry (#)": {
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+ "do_not_merge": true,
165
+ "allow_empty": true,
89
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  "merge_pointer": "/shipping_entry_number",
90
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  "type_ref": "sample.json#properties/shipping_entry_number"
91
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  },
@@ -142,16 +219,35 @@
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  "merge_pointer": "/type_of_tumor_sample",
143
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  "type_ref": "sample.json#properties/type_of_tumor_sample"
144
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  },
222
+ "description of sample": {
223
+ "merge_pointer": "/description_of_sample",
224
+ "type_ref": "sample.json#properties/description_of_sample",
225
+ "allow_empty": true
226
+ },
145
227
  "sample collection procedure": {
146
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  "merge_pointer": "/sample_collection_procedure",
147
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  "type_ref": "sample.json#properties/sample_collection_procedure"
148
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  },
231
+ "sample collection procedure other": {
232
+ "merge_pointer": "/sample_collection_procedure_other",
233
+ "type_ref": "sample.json#properties/sample_collection_procedure_other",
234
+ "allow_empty": true
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+ },
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+ "type of primary container": {
237
+ "merge_pointer": "/type_of_primary_container",
238
+ "type_ref": "sample.json#properties/type_of_primary_container"
239
+ },
240
+ "type of primary container other": {
241
+ "merge_pointer": "/type_of_primary_container_other",
242
+ "type_ref": "sample.json#properties/type_of_primary_container_other",
243
+ "allow_empty": true
244
+ },
149
245
  "core number": {
150
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  "merge_pointer": "/core_number",
151
247
  "type_ref": "sample.json#properties/core_number",
152
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  "allow_empty": true
153
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  },
154
- "fixation/stabilization type": {
250
+ "fixation stabilization type": {
155
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  "merge_pointer": "/fixation_stabilization_type",
156
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  "type_ref": "sample.json#properties/fixation_stabilization_type"
157
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  },
@@ -216,4 +312,4 @@
216
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  }
217
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  }
218
314
  }
219
- }
315
+ }
cidc_schemas/schemas/templates/manifests/tumor_tissue_dna_template.json CHANGED
@@ -41,16 +41,16 @@
41
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  "type_ref": "shipping_core.json#properties/tracking_number",
42
42
  "allow_empty": true
43
43
  },
44
- "account number": {
45
- "merge_pointer": "/account_number",
46
- "type_ref": "shipping_core.json#properties/account_number",
47
- "allow_empty": true
48
- },
49
44
  "shipping condition": {
50
45
  "merge_pointer": "/shipping_condition",
51
46
  "type_ref": "shipping_core.json#properties/shipping_condition",
52
47
  "allow_empty": true
53
48
  },
49
+ "shipping condition other": {
50
+ "merge_pointer": "/shipping_condition_other",
51
+ "type_ref": "shipping_core.json#properties/shipping_condition_other",
52
+ "allow_empty": true
53
+ },
54
54
  "date shipped": {
55
55
  "merge_pointer": "/date_shipped",
56
56
  "type_ref": "shipping_core.json#properties/date_shipped",
@@ -66,14 +66,89 @@
66
66
  "type_ref": "shipping_core.json#properties/quality_of_shipment",
67
67
  "allow_empty": true
68
68
  },
69
- "ship from": {
70
- "merge_pointer": "/ship_from",
71
- "type_ref": "shipping_core.json#properties/ship_from",
69
+ "ship from sender person name": {
70
+ "merge_pointer": "/ship_from_sender_person_name",
71
+ "type_ref": "shipping_core.json#properties/ship_from_sender_person_name",
72
+ "allow_empty": true
73
+ },
74
+ "ship from sender email": {
75
+ "merge_pointer": "/ship_from_sender_email",
76
+ "type_ref": "shipping_core.json#properties/ship_from_sender_email",
72
77
  "allow_empty": true
73
78
  },
74
- "ship to": {
75
- "merge_pointer": "/ship_to",
76
- "type_ref": "shipping_core.json#properties/ship_to",
79
+ "ship from sender phone": {
80
+ "merge_pointer": "/ship_from_sender_phone",
81
+ "type_ref": "shipping_core.json#properties/ship_from_sender_phone",
82
+ "allow_empty": true
83
+ },
84
+ "ship from name": {
85
+ "merge_pointer": "/ship_from_name",
86
+ "type_ref": "shipping_core.json#properties/ship_from_name",
87
+ "allow_empty": true
88
+ },
89
+ "ship from street1": {
90
+ "merge_pointer": "/ship_from_street1",
91
+ "type_ref": "shipping_core.json#properties/ship_from_street1",
92
+ "allow_empty": true
93
+ },
94
+ "ship from street2": {
95
+ "merge_pointer": "/ship_from_street2",
96
+ "type_ref": "shipping_core.json#properties/ship_from_street2",
97
+ "allow_empty": true
98
+ },
99
+ "ship from city": {
100
+ "merge_pointer": "/ship_from_city",
101
+ "type_ref": "shipping_core.json#properties/ship_from_city",
102
+ "allow_empty": true
103
+ },
104
+ "ship from state": {
105
+ "merge_pointer": "/ship_from_state",
106
+ "type_ref": "shipping_core.json#properties/ship_from_state",
107
+ "allow_empty": true
108
+ },
109
+ "ship from zip": {
110
+ "merge_pointer": "/ship_from_zip",
111
+ "type_ref": "shipping_core.json#properties/ship_from_zip",
112
+ "allow_empty": true
113
+ },
114
+ "ship from country": {
115
+ "merge_pointer": "/ship_from_country",
116
+ "type_ref": "shipping_core.json#properties/ship_from_country",
117
+ "allow_empty": true
118
+ },
119
+ "ship to name": {
120
+ "merge_pointer": "/ship_to_name",
121
+ "type_ref": "shipping_core.json#properties/ship_to_name",
122
+ "allow_empty": true
123
+ },
124
+ "ship to street1": {
125
+ "merge_pointer": "/ship_to_street1",
126
+ "type_ref": "shipping_core.json#properties/ship_to_street1",
127
+ "allow_empty": true
128
+ },
129
+ "ship to street2": {
130
+ "merge_pointer": "/ship_to_street2",
131
+ "type_ref": "shipping_core.json#properties/ship_to_street2",
132
+ "allow_empty": true
133
+ },
134
+ "ship to city": {
135
+ "merge_pointer": "/ship_to_city",
136
+ "type_ref": "shipping_core.json#properties/ship_to_city",
137
+ "allow_empty": true
138
+ },
139
+ "ship to state": {
140
+ "merge_pointer": "/ship_to_state",
141
+ "type_ref": "shipping_core.json#properties/ship_to_state",
142
+ "allow_empty": true
143
+ },
144
+ "ship to zip": {
145
+ "merge_pointer": "/ship_to_zip",
146
+ "type_ref": "shipping_core.json#properties/ship_to_zip",
147
+ "allow_empty": true
148
+ },
149
+ "ship to country": {
150
+ "merge_pointer": "/ship_to_country",
151
+ "type_ref": "shipping_core.json#properties/ship_to_country",
77
152
  "allow_empty": true
78
153
  }
79
154
  }
@@ -86,6 +161,8 @@
86
161
  "data_columns": {
87
162
  "IDs": {
88
163
  "entry (#)": {
164
+ "do_not_merge": true,
165
+ "allow_empty": true,
89
166
  "merge_pointer": "/shipping_entry_number",
90
167
  "type_ref": "sample.json#properties/shipping_entry_number"
91
168
  },
@@ -142,16 +219,35 @@
142
219
  "merge_pointer": "/type_of_tumor_sample",
143
220
  "type_ref": "sample.json#properties/type_of_tumor_sample"
144
221
  },
222
+ "description of sample": {
223
+ "merge_pointer": "/description_of_sample",
224
+ "type_ref": "sample.json#properties/description_of_sample",
225
+ "allow_empty": true
226
+ },
145
227
  "sample collection procedure": {
146
228
  "merge_pointer": "/sample_collection_procedure",
147
229
  "type_ref": "sample.json#properties/sample_collection_procedure"
148
230
  },
231
+ "sample collection procedure other": {
232
+ "merge_pointer": "/sample_collection_procedure_other",
233
+ "type_ref": "sample.json#properties/sample_collection_procedure_other",
234
+ "allow_empty": true
235
+ },
236
+ "type of primary container": {
237
+ "merge_pointer": "/type_of_primary_container",
238
+ "type_ref": "sample.json#properties/type_of_primary_container"
239
+ },
240
+ "type of primary container other": {
241
+ "merge_pointer": "/type_of_primary_container_other",
242
+ "type_ref": "sample.json#properties/type_of_primary_container_other",
243
+ "allow_empty": true
244
+ },
149
245
  "core number": {
150
246
  "merge_pointer": "/core_number",
151
247
  "type_ref": "sample.json#properties/core_number",
152
248
  "allow_empty": true
153
249
  },
154
- "fixation/stabilization type": {
250
+ "fixation stabilization type": {
155
251
  "merge_pointer": "/fixation_stabilization_type",
156
252
  "type_ref": "sample.json#properties/fixation_stabilization_type"
157
253
  },
@@ -258,4 +354,4 @@
258
354
  }
259
355
  }
260
356
  }
261
- }
357
+ }